The universal flood and the Ark of Noah cause problems for you because you deny the Word of God and choose not to exercise faith in God.
Why does 2+2=4? Who knows. It just does. How did God assemble all the animals and feed them? Well, God knows, but then again, He's God. There are a number of possible explanations, but listing them would be pure speculation. The simple fact is that you have chosen to not believe in the written account of history.